title: Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

city: Vienna

first: Luis Enrique

last: Cabrera Quio

address: Campus Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: Post-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3’-to-5’ degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-to-embryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important post-transcriptional regulator during the oocyte-to-embryo transition.

overall_design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte-to-embryo transition. Every time point from each genotype was performed in triplicates.

first: Luis

middle: E

first: Alexander

last: Schleiffer

first: Karl

last: Mechtler

first: Andrea

last: Pauli


title: YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation (ChIP-seq)

status: Public on Feb 18 2021

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The YAP and TAZ paralogues, the ultimate effectors of the Hippo signaling pathway, are  deregulated in many cancer types. They are transcriptional co-activators that are  recruited to their target sites, primarily by TEAD proteins. Here, we show that YAP and  TAZ are also recruited by JUNB and STAT3, key factors that mediate an epigenetic  switch linking inflammation to breast cellular transformation. YAP and TAZ directly  interact with JUNB and STAT3 via a WW domain that is important for transformation,  co-occupy many target sites in vivo via the sequence motifs of AP-1 and (to a lesser extent) STAT3, and stimulate transcriptional activation by AP-1 proteins. A small minority of  target sites are YAP- or TAZ-specific, and they are associated with different sequence  motifs and gene classes. YAP/TAZ, JUNB, and STAT3 directly regulate a common set  of target genes that overlap, but are distinct from, those regulated by YAP/TAZ and  TEADs. The set of target genes regulated by YAP/TAZ, STAT3, and JUNB is associated  with poor survival in breast cancer patients with the triple-negative form of the disease.

overall_design: YAP/TAZ, AP-1 and STAT3 transcriptional regulation in breast cancer

first: Zhiping

last: Weng

first: Lizhi

last: He

first: Henry

last: Pratt

first: Fengxiang

last: Wei

first: Mingshi

last: Gao


title: YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Toxoplasma and Eimeria co-opt the host cFos expression for intracellular development in mammalian cells

status: Public on Jan 27 2021

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

summary: Successful asexual reproduction of intracellular pathogens depend on their potential to exploit host resources and subvert antimicrobial defense. Here, we deployed two prevalent intracellular parasites of mammalian cells, namely Toxoplasma gondii and Eimeria falciformis, to identify the potential host determinants of infection. Expression analyses of the young adult mouse colonic (YAMC) epithelial cells showed regulation of several distinct transcripts upon infection by either parasite, indicating that closely-related pathogens program their intracellular niches in notably adaptive manner. Conversely, parasitized mouse embryonic fibroblasts (MEFs) exhibited a divergent transcriptome compared to corresponding YAMC cells, suggesting that individual host cells mount fairly discrete response while encountering a given pathogen. Among a limited set of factors similarly regulated by both parasites, we identified cFos, a master transcription factor, that was consistently induced throughout infection. Indeed, the asexual development of T. gondii and E. falciformis was severely impaired in MEF cells lacking cFos expression. Last but not least, our comparative transcriptomics of the parasitized MEFs (wild-type and cFos-/- mutant) and YAMC epithelial cells disclosed a cFos-network, underlying signal transduction cascades, as well as a repertoire of nucleotides-binding and ion-binding proteins, which are likely co-opted by coccidian pathogens to acclimatize the mammalian host environment.

overall_design: Microarray experiments were performed as dual-color hybridizations on SurePrint G3 Mouse Gene Expression v2 Microarrays  (Agilent-014868). To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Bingjian

last: Ren

first: Manuela

last: Schmid

first: Richard

last: Lucius

first: Emanuel

last: Heitlinger

first: Nishith

last: Gupta


title: Astrocytic ApoE reprograms neuronal cholesterol metabolism and histone acetylation mediated memory

status: Public on Jan 26 2021

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

country: China

institute: University of Science and Technology of China


title: Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization [ATAC-seq]

status: Public on Jan 22 2021

city: Ann Arbor

first: Eleanor

middle: Josephine

last: Clowney

state: MI

address: 1105 North University, 4218

department: MCDB

institute: University of Michigan

summary: Chromatin accessibility of neurons comprising most of the central brain courtship circuit in adult male Drosophila brains, with sex and cell-type control populations.

overall_design:
Profiles of chromatin accessibility were generated from adult male and female central brain neurons sorted on transcriptional status of fruitless. Fru+ neurons, excluding fru+ Kenyon cells, were isolated by sorting for GFP+ neurons (MB247-GAL80, FruP1-GAL4 > UAS::mCD8-GFP). A matched number of cells from the unlabeled population (GFP-) were collected.
Please note that each '*Pooled.bed' file was generated from both replicates and is linked to the corresponding R1 sample records.

first: E

middle: J

first: Margarita

middle: V

last: Brovkina


status: Public on Jan 28 2021

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

institute: 武汉大学

summary:
mRNA transcriptome sequencing of tumor bearing lungs from KrasLSL-G12D/+Lkb1fl/fl, KrasLSL-G12D/+Lkb1fl/flIl1f9-/-(KL9) and KrasLSL-G12D/+Lkb1fl/flIl1f5-/-(KL5) or KrasLSL-G12D/+Tp53fl/fl, KrasLSL-G12D/+Tp53fl/flIl1f9-/-(KP9) and KrasLSL-G12D/+Tp53fl/flIl1f5-/-(KP5) after 10 weeks Ad-cre injection
Tumor-burdened lungs from KL/KL5/KL9 mice and KP/KP5/KP9 mice were perfused through alveolar lavage and cardiac lavage with PBS, dry it quickly, and then homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA  was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene). Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev). All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read. Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).

overall_design: KL(n=2) , KL5(n=2) and KL9(n=2) mice were used,respectively;KP(n=2), KP5(n=3) and KP9(n=3) were used.respectively

first: P

last: Wang

first: W

last: Yang

first: B

last: Zhong


title: Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization


title: Global transcriptome analysis of Stenotrophomonas maltophilia in response to human body temperature

status: Public on Jan 11 2021

city: Chandigarh

first: Prabhu

middle: B

last: Patil

state: Chandigarh

address: Sector 39 A

country: India

institute: CSIR Institute of Microbial Technology Chandigarh

summary: Stenotrophomonas maltophilia is an emerging multidrug resistance opportunistic pathogen affecting immunocompromised and hospitalized patients. S. maltophilia is an environmental bacterium which adapts to human body and causing infection. S. rhizophilia, a non-pathogenic and phylogenetic neighbour of S. maltophilia is unable to grow at human body temperature. Thus, to understand molecular mechanism underlying the adaptation of S. maltophilia at human body temperature, we performed the comparative transcriptome analysis of S.maltophilia at 28 °C (representative for the environmental niches) and 37 °C (representative for human body) by using RNA-Seq. The major temperature-induced genes include genes for Type IV secretion system, aerotaxis, and cation diffusion facilitator family transporter suggesting its potential role in the adaptation and virulence of S. maltophilia. The downregulated genes at 37 °C includes the genes for the cell motility, energy generation and metabolism, lipid metabolism, translation, amino acid metabolism and transport, replication and repair, inorganic ion and transport metabolism lipid metabolism, coenzyme metabolism.

overall_design: Comparative transcriptome analysis of S.maltophilia at 28°C as a temperature representative for the environmental niches and 37 °C for the human body by using RNA-Seq. Total RNA was isolated by growing the cells at 28°C and 37°C  in triplicate, ribodepleted RNA samples, Illumina library constructed of cDNA and sequenced on Illumina Miseq.

middle: P

first: S

last: Kumar

last: Midha


title: Performance of a highly scalable and extraction-free RNA-seq method

city: Iowa city

first: Alejandro

middle: Pezzulo

last: Colmenares

state: Iowa

address: 169 Newton Road

department: Internal medicine

institute: University of Iowa

summary: RNA-seq workflows have become progressively more efficient over time however, RNA extraction still remains a significant bottleneck. For small numbers of sample, highly efficient RNA extraction is simple to perform but becomes costly and laborious at the scale of hundreds of samples. Our prior work has demonstrated that qPCR can be accurately performed using bulk cells samples lysate instead of RNA extraction. We combined this method with the recently developed simple method for rapid RNA-seq library prep; Smart-3SEQ (Foley et al., 2019) and hypothesized that bulk RNA-seq can be performed in a multi-well plate format, and at low cost by performing RNA-seq library prep cDNA synthesis using in-lysate RNA followed by Smart-3SEQ. The result shows success of our approach in various levels: 1) all quality control measures were achieved, 2) Gene expression profiles, gene differential expression and the response patterns reported by in-lysate and purified RNA library highly correlate with each other, and 3) in-lysate RNA-seq library prep performed similar to the gold standard used here (Illumina Truseq) for DEG calling.

overall_design: Human primary dermal fibroblasts from 6 donors were exposed to DMSO(vehicle), calmidazolium(10 μM)  or fludrocortisone(10 μM) for 6 hours. For purified_RNA samples, RNA extraction was done and for in-lysate RNA, cultures were treated with Igepal CA 630(0.3%)/BSA(0.1%) buffer for 5 min and supernatant was used for library prep. For both methods, cDNA libraries were prepared using Smart-3SEQ library prep and sequenced. For our gold standard, extracted RNA was used to prepare Illumina TruSeq libraries and then sequenced. Comparison is to be made between Purified_RNA and in-lysate RNA prepared with Smart-3SEQ library and how these data compare to the gold standard.

first: Shreya

last: Ghimire

first: Andrew

middle: L

last: Thurman

first: Carley

middle: G

last: Stewart

middle: A

last: Pezzulo


title: Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization [RNA-Seq]

summary: Gene expression profile of neurons comprising most of the central brain courtship circuit in adult male Drosophila brains, with sex and cell-type control populations.

overall_design: Profiles of gene expression were generated from adult male and female central brain neurons sorted on transcriptional status of fruitless. Fru+ neurons, excluding fru+ Kenyon cells, were isolated by sorting for GFP+ neurons (MB247-GAL80, FruP1-GAL4 > UAS::mCD8-GFP). A matched number of cells from the unlabeled population (GFP-) were collected.


title: Single cell transcriptomic data from MGE-derived interneurons purified from postnatal day 18-21 frontal cortex and hippocampus of wild type and MGE-specific GRIN1-knockout mice.

status: Public on Jan 25 2021

city: Bethesda

first: Vivek

last: Mahadevan

state: Maryland

address: 35, Convent Drive

department: aSection on Cellular and Synaptic Physiology

institute: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)

summary: Medial ganglionic eminence (MGE)-derived parvalbumin (PV)+, somatostatin (SST)+ and Neurogliaform (NGFC)-type cortical and hippocampal interneurons, have distinct molecular, anatomical and physiological properties. However, the molecular mechanisms regulating their diversity remain poorly understood. Here, via single-cell transcriptomics, we show that the obligate NMDA-type glutamate receptor (NMDAR) subunit gene Grin1 mediates subtype-specific transcriptional regulation of gene expression in MGE-derived interneurons, leading to altered subtype identities. Notably, MGE-specific conditional Grin1 loss results in a systemic downregulation of diverse transcriptional, synaptogenic and membrane excitability regulatory programs. These widespread gene expression abnormalities mirror aberrations that are typically associated with neurodevelopmental disorders, particularly schizophrenia. Our study hence provides a roadmap for the systematic examination of NMDAR signaling in interneuron subtypes, revealing potential MGE-specific genetic targets that could instruct future therapies of psychiatric disorders.

overall_design: Frontal cortex and hippocampus of wild-type and MGE-specific GRIN1-knockout mice have been dissected and FACS-sorted Nkx2.1-cell-type specific cells (Td-tomato positive)

first: Apratim

last: Mitra

first: Yajun

last: Zhang

first: Areg

last: Peltekian

first: Ramesh

last: Chittajallu

first: Caroline

last: Esnault

first: Dragan

last: Maric

first: Christopher

last: Rhodes

first: Kenneth

last: Pelkey

first: Ryan

last: Dale

first: Timothy

last: Petros

first: Chris

last: McBain


title: NFκB dynamics determine the stimulus-specificity of epigenomic reprogramming in macrophages

status: Public on Jan 01 2021

city: Los Angeles

first: Quen

last: Cheng

state: CA

address: 611 Charles E Young Dr E

institute: UCLA

summary: The epigenome defines the cell type, but also possesses plasticity to tune gene expression in the context of extracellular cues. This tuning is evident in immune sentinel cells such as macrophages, which respond to pathogens and cytokines with phenotypic shifts driven by epigenomic reprogramming. Recent studies indicate that this reprogramming arises from the activity of transcription factors including nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB). NFκB binds not only to available enhancers but may also produce de novo enhancers in previously silent areas of the genome. Here, we show that NFκB reprograms the macrophage epigenome in a stimulus-specific manner, in response only to a subset of pathogen-derived stimuli. The basis for these surprising differences lies in the stimulus-specific temporal dynamics of NFκB activity. In response to different stimuli, NFκB enters the nucleus with variable speed, amplitude, and duration, and may oscillate between the nucleus and cytoplasm. These dynamical features combine to specify the identity and dose of a given stimulus. We demonstrate through live cell imaging, mathematical modeling, and genetic perturbations that NFκB promotes open chromatin and formation of de novo enhancers most strongly when its dynamics are non-oscillatory. These de novo enhancers result in the activation of additional response genes. We propose a mechanistic paradigm in which the temporal dynamics of transcription factors are a key determinant of their capacity to control epigenomic reprogramming, thus enabling the formation of stimulus-specific memory in innate immune sentinel cells.

overall_design: Sequencing data from murine bone marrow-derived macrophages, comparing different TLR stimuli and using genetic perturbations of NFκB signaling dynamics. H3K4me1 ChIP-seq (41 samples), ATAC-seq (36 samples), mRNA-seq (19 samples).

first: Sho

last: Ohta

first: Katherine

middle: M

last: Sheu

first: Roberto

last: Spreafico

first: Adewunmi

last: Adelaja

first: Brooks

last: Taylor

first: Alexander

last: Hoffmann


title: Cis-Regulatory Element Hijacking by Structural Variants Overshadows Topological Changes in Primary Prostate Cancer

status: Public on Jan 07 2021

city: Mississauga

first: James

middle: R

last: Hawley

state: Ontario

address: 7070 Mississauga Road

department: Computational Sciences

country: Canada

institute: Roche Canada

summary: Prostate cancer is a heterogeneous disease whose progression is linked to genome instability. However, the impact of this instability on the non-coding genome and its three-dimensional organization to aid progression is unclear. Using primary benign and tumor tissue, we find a high concordance in higher order three-dimensional genome organization. This concordance argues for constraints to the topology of prostate tumor genomes. Nonetheless, we identified changes in focal chromatin interactions, typical of loops bridging non-coding cis-regulatory elements, and showed how structural variants can induce these changes to guide cis-regulatory element hijacking. Such events resulted in opposing differential expression of genes found at antipodes of rearrangements. Collectively, these results argue that changes to focal chromatin interactions, as opposed to higher order genome organization, allow for aberrant gene regulation and are repeatedly mediated by structural variants in primary prostate cancer.

overall_design:
Hi-C sequencing in primary prostate tissues, both benign and tumour

**The raw data not provided due to patient privacy. Files will be uploaded to the European Genome/Phenome Archive (Accession EGAS00001005014).

first: Stanley

last: Zhou

first: Mathieu

last: Lupien


title: Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line [Seq]

status: Public on Dec 31 2020

city: Kunming

first: Jinlong

last: Huo

state: Yunnan

address: Jin-hei

department: Faculty of Animal Science and Technology

institute: Yunnan Agricultural University

type: Genome variation profiling by high throughput sequencing

summary: We sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, the Banna Minipig Inbred Line (BMI). we conducted whole genome screening using next generation sequencing (NGS) technology and performed SNP calling using Sus Scrofa genome assembly Sscrofa11.1.

overall_design: Detection of genome homozygosity of Banna Minipig Inbred Line (BMI).

first: Liqing

last: Zhang


title: Astrocytic ApoE reprograms neuronal cholesterol metabolism and histone acetylation mediated memory [RNA-seq]

first: Qiang

last: Liu

summary: We report the high-throughput sequencing of RNA expression in cultured neurons and the brain. We report the high-throughput sequencing of mRNA expression in primary cultured Neurons.

overall_design: Examination of RNA expression pattern in treated Neurons and the brain. Examination of RNA expression pattern in treated Neurons.

first: Juan

first: Xiaohui

last: Li


title: The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [RNA-seq]

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

institute: Max Perutz Labs

summary: Transcriptomic analysis of wild type C. albicans and a HIR1 gene deletion mutant during nutrient rich growth (YPD) and upon the shift to nitrogen starvation in yeast carbon base medium supplemented with BSA (YCB-BSA medium).

overall_design: RNA Sequencing was performed of wild type and HIR1-deficient Candida albicans grown overnight in YPD medium (nitrogen rich conditions) and after 4 hours and 8 hours of growth in YCB-BSA medium where BSA is the major nitrogen source. Cells were harvested after each time point or prior transfer to YCB-BSA medium for RNA isolation. Three biological replicates for each condition were performed.

first: Theresia

last: Mair

first: Karl

last: Kuchler


title: Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line


title: Dual inhibition of histone deacetylases and the mechanistic target of rapamycin promotes apoptosis in cell line models of uveal melanoma

status: Public on Dec 30 2020

first: Robert

last: Robey

state: MD

address: 37 Convent Drive Rm 2112

institute: NCI

summary:
We investigated the effects of HDACi romidepsin and mTORi AZD-8055 in uveal melanoma cell line Mel202.
Uveal melanomas harbor mutations in the GNAQ or GNA11 genes that activate survival pathways. As previous studies found that Ras-mutated cell lines were uniquely vulnerable to a combination of inhibitors of Ras-activated survival pathways and the histone-deacetylase inhibitor (HDI) romidepsin, we investigated whether this combination would be effective in models of uveal melanoma. A small-scale screen of inhibitors of bromodomain-containing protein 4 (BRD4, OTX-015), extracellular signal-related kinase (ERK, ulixertinib), mammalian target of rapamycin (mTOR, AZD-8055) or phosphoinositide 3-kinase (PI3K, GDC-0941) combined with a clinically-relevant administration of romidepsin was performed on a panel of uveal melanoma cell lines (92-1, Mel202, MP38, and MP41) and apoptosis was quantified by flow cytometry after 48 hr. RNA sequencing analysis was performed on Mel202 cells treated with romidepsin alone, the mTOR inhibitor AZD-8055 or the combination, and protein changes were validated    by immunoblot. We found combining AZD-8055 with romidepsin was the most effective combination in inducing apoptosis in the cell lines. Increased caspase-3 and PARP cleavage were noted in the MP41 and Mel202 cell lines when they were treated with romidepsin and mTOR inhibitors. RNA sequence analysis of Mel202 cells revealed that apoptosis was the most affected pathway in the romidepsin/AZD-8055 treated cells. Increases in pro-apoptotic BCL2L11 and decreases in anti-apoptotic BIRC5 and BCL2L1 proteins noted in the sequencing analysis were confirmed at the protein level. Our data suggest that romidepsin in combination with mTOR inhibition could be an effective treatment strategy against uveal melanoma due in part to changes in apoptotic proteins.

overall_design: Uveal melanoma cell line Mel202 was either untreated or treated with 25 ng/mL romidepsin, 1 uM AZD-8055, or a combination of the two for 6 hours.

first: Ruchi

last: Patel

last: Curt

first: Christina

last: Fitzsimmons

first: Pedro

last: Batista

first: Susan

last: Bates

first: Michael

last: Gottesman

middle: W

first: Joanna

last: Thomas


title: The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans


title: Analysis of Whole Genome Sequence and Genome-wide SNPs in Highly Inbred Pigs [Array]

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We conducted a genome wide survey of single nucleotide polymorphisms (SNPs) using the porcine 60 K SNP chips on inbred pigs

overall_design: The Illumina PorcineSNP60 BeadChip (Illumina, San Diego, CA) was used to genotype the Banna Mini-pig Inbred Line (BMI)


title: Stage-specific miRNA expression profiling during menstrual cycle in endometriosis and non-endometriosis patients

status: Public on Dec 29 2020

city: Tehran

first: mehrdad

last: noruzinia

address: jalal ale ahmad

country: Iran

institute: Tarbiat Modares University

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of this research was to determined the plasma miRNA expresion profile in each stage of the endometriosis during menstrual cycle.

overall_design: According to clinical findings, stage, and phase of sampling, all volunteers were divided into six symmetric subgroups (P1,P2,P3,P4,P5 and P6), each containing 5 patients. Similarly, healthy subjects were classified into three subgroups (N1,N2 and N3) according to their phase of sampling

first: Mehrdad

last: Noruzinia


title: The histone chaperone HIR establishes chromatin states controling nitrogen assimilation and virulence in Candida albicans [ATAC-seq]

summary: ATAC-seq analysis of wild type C. albicans and a HIR1 gene deletion mutant during nutrient rich growth (YPD) and upon the shift to nitrogen starvation in yeast carbon base medium supplemented with BSA (YCB-BSA medium).

overall_design: ATAC-seq was performed of wild type and HIR1-deficient Candida albicans grown overnight in YPD medium (nitrogen rich conditions) and after 4 hours and 8 hours of growth in YCB-BSA medium where BSA is the major nitrogen source. Cells were harvested after each time point or prior transfer to YCB-BSA medium, subjected to spheroplasting, tagmentation and ATAC-seq library preparation. Three biological replicates for each condition were performed.

last: Tscherner


title: RNA-Sequece Analysis of si-THAP7-AS1 and SI-NC IN MDA-MB-231 cells

status: Public on Jan 17 2021

city: Jinan

first: Haiting

address: West Wenhua Road 44

institute: Shandong University

summary: RNA-seq was used to analyze the differential expression of mRNAs between si-THAP7-AS1 and si-NC 231 cells.

overall_design: THAP7-AS1 was knocked down by transfection with THAP7-AS1 Smart Silencer in 231 cells. After 48h, we obtained the samples.

first: Hai-ting

first: Sen

first: Xiang-yu

last: Guo

first: Guo-hao

last: Zhang


title: Temporal transcriptomic analysis of five Staphylococcus aureus strains' biofilms and planktonic counterparts

status: Public on Dec 22 2020

city: Tampa

first: Lindsey

middle: N

last: Shaw

state: FL

address: 4202 E Fowler Avenue

department: CMMB

institute: University of South Florida

summary: Differential expression of five S. aureus biofilms versus their planktonic counterparts at 5 h, 10 h, and 24 h.

overall_design: S. aureus biofilms were formed in TSB using 96-well plates for five S. aureus strains: N315 (USA100), MRSA252 (USA200), LAC (USA300), MW2 (USA400), NRS385 (USA500). Biofilm samples and their planktonic counterparts were collected in biological triplicate at 5 h, 10 h, and 24 h. Each sample was generated by pooling three independent biological replicate RNA preps.

first: Brooke

last: Tomlinson


title: Time course transcriptomic analysis of human melanoma A375 cells dying of immunogenic or non immunogenic apoptosis

status: Public on Dec 17 2020

city: Leuven

first: Nicole

last: rufo

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: We set out to investigate the transcriptional profile of cancer cells responding to mitoxantrone (MTX) or hypericin-based photodynamic therapy (Hyp-PDT), as prototypes of immunogenic treatments compared to cisplatin (CDDP), considered a poorly immunogenic chemotherapeutic. We isolated the bulk-RNA of the treated cells, at 0 hr (untreated) and 4 hr (pre-apoptotic), 10 hr (early apoptotic) and 20 hr (late apoptotic) post-treatment, and compared it to their respective time-matched untreated controls. Differential gene expression analysis revealed that MTX and Hyp-PDT significantly upregulated the transcription of several genes as early as 4 hr post-treatment, whereas responses to CDDP treatment occurred mainly at the later time points and were associated with a predominant transcript downregulation. Bioinformatics analyses showed pathways relative to chemokine signaling and inflammation as significantly associated selectively to cells dying in an immunogenic fashion.

overall_design: mRNA profiles of human melanoma A375p cells 4 hours, 10 hours and 20 hours after treatment with immunogenic treatments (MTX, Hyp-PDT) and non-immunogenic treatments (CDDP) and time matched untreated controls

last: Rufo

first: Patrizia

last: Agostinis


title: Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients

status: Public on Dec 15 2020

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

summary: To understand the cellular composition and transcriptional phenotype of fibrotic lung tissue we performed single-cell RNA-seq on stromal, immune, epithelial, and endothelial cell populations from human lung explants. Tissue was collected from normal control lungs, patients with idiopathic pulmonary fibrosis (IPF), and patients with systemic sclerosis associated interstitial lung disease (SSc-ILD). Using the 10X Genomics Chromium platform, we generated transcriptional profiles of approximately 200,500 cells across 4 IPF, 3 SSc-ILD and 3 normal control lungs.

overall_design: Fresh lung explant tissue from 4 IPF patients, 3 SSc-ILD patients, or 3 transplant rejection controls were stored in complete media on wet ice overnight. Tissue was washed, minced, digest and sorted via FACS into separate preparations of EPCAM+, CD31+, CD45+, and triple negative (EPCAM- CD31-, CD45-) cells. For a limited number of samples, unsorted, CD90+, EPCAM+SAbGAL+/- or EPCAM+HT2-280+/- preparations were also made. Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit v2, followed by sequencing on the Illumina HiSeq 4000 platform.

first: Daryle

last: DePianto

first: Katrina

last: Morshead

first: Kai-Hui

last: Sun

first: Paul

last: Wolters

first: Joseph

last: Arron


title: Cellular and extracellular miRNA profiles of pre-ovulatory follicles indicate signalling disturbances in polycystic ovaries

city: Tallinn

first: Ilmatar

last: Rooda

address: Akadeemia tee 15

department: Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

summary: Cell-free RNAs have been used as diagnostic disease markers describing the state of tissue environment. The origin and potential functions of such RNAs in human pre-ovulatory follicle, the environment of oocyte maturation, are unclear. We aimed to describe the small RNA profiles of three follicular compartments of the same follicle: mural granulosa cells (MGC), cell-free follicular fluid (FF) and extracellular vesicles (EV) of the FF. Focusing on microRNAs, their signatures and regulated pathways were compared between infertile women with polycystic ovaries and fertile control group.

overall_design: miRNA profiles of pre-ovulatory follicle mural granulosa, whole cell-free follicular fluid and extracellular vesicles of the follicular fluid

first: Mehedi

last: Hasan

first: Kristine

last: Roos

first: Janeli

last: Viil

first: Olli-Pekka

last: Smolander

first: Andres

last: Salumets

first: Alireza

last: Fazeli

first: Agne

last: Velthut-Meikas


title: DDX3X Loss is Associated with Aggressive Phenotypes in Non-Hodgkin’s Lymphomas

status: Public on Dec 25 2020

city: Singapore

first: Kizhakeyil

last: Atish

state: Singapore

address: Mandalay road 11

country: Singapore

institute: Nanyang Technological University

summary: We demonstrate that DDX3X inactivation/depletion in NHL cell lines causes enhanced proliferation, invasion and chemoresistance.

overall_design: We performed RNAseq analsysis of control versus DDX3X depleted HuT78, control versus DDX3X depleted SNK1 and WT versus mutant DDX3X-R475C expressing U2392.

first: Poh

middle: Z

last: Sheng

first: Navin

middle: K

last: Verma


title: In-depth clinical and biological exploration of DNA Damage Immune Response (DDIR) as a biomarker for oxaliplatin use in colorectal cancer

city: Oxford

first: Andrew

last: Blake

state: Oxfordshire, UK

address: Old Road Campus

country: United Kingdom

institute: Department of Oncology

summary:
Purpose: The DNA Damage Immune Response (DDIR) assay was developed in breast cancer (BC) based on biology associated with deficiencies in homologous recombination and Fanconi Anemia (HR/FA) pathways. A positive DDIR call identifies patients likely to respond to platinum-based chemotherapies in breast and oesophageal cancers. In colorectal cancer (CRC) there is currently no biomarker to predict response to oxaliplatin. We tested the ability of the DDIR assay to predict response to oxaliplatin-based chemotherapy in CRC and characterised the biology in DDIR-positive CRC.
Methods: Samples and clinical data were assessed according to DDIR status from patients who received either 5FU or FOLFOX within the FOCUS trial (n=361, stage 4), or neo-adjuvant FOLFOX in the FOxTROT trial (n=97, stage 2/3). Whole transcriptome, mutation and immunohistochemistry data of these samples were used to interrogate the biology of DDIR in CRC.
Results: Contrary to our hypothesis, DDIR negative patients displayed a trend towards improved outcome for oxaliplatin-based chemotherapy compared to DDIR positive patients. DDIR positivity was associated with Microsatellite Instability (MSI) and Colorectal Molecular Subtype 1 (CMS1). Refinement of the DDIR signature, based on overlapping interferon-related chemokine signalling associated with DDIR positivity across CRC and BC cohorts, further confirmed that the DDIR assay did not have predictive value for oxaliplatin-based chemotherapy in CRC.
Conclusions: DDIR positivity does not predict improved response following oxaliplatin treatment in CRC. However, data presented here suggests the potential of the DDIR assay in identifying immune-rich tumours that may benefit from immune checkpoint blockade, beyond current use of MSI status.

overall_design: 361 Samples analysed, no replicates nor reference samples used


title: Single cell epigenomics reveals mechanisms of human cortical development

status: Public on Dec 11 2020

city: San Francisco

first: Ryan

last: Ziffra

institute: UCSF

summary: During mammalian development, chromatin state differences coincide with cellular differentiation and reflect changes in the gene regulatory landscape. In the developing brain, cell fate specification and topographic identity play important roles in defining cell identity and confer selective vulnerabilities to neurodevelopmental disorders. To identify cell type specific chromatin accessibility patterns in the developing human brain, we used a single cell assay for transposase accessibility by sequencing (scATAC-seq) in primary human forebrain tissue samples. We applied unbiased analyses to identify genomic loci that undergo extensive cell type- and brain region-specific changes in accessibility during neurogenesis and an integrative analysis to predict cell type specific candidate regulatory elements. We found that cerebral organoids recapitulate most putative cell type-specific enhancer accessibility patterns but lack many cell type specific open chromatin regions found in vivo. Systematic comparison of chromatin accessibility across brain regions revealed an unexpected diversity among neural progenitor cells in the cerebral cortex and implicate retinoic acid signaling in the specification of prefrontal cortex neuronal lineage identity. Together, our results reveal the important contribution of chromatin state to the emerging patterns of cell type diversity and cell fate specification and provide a blueprint for evaluating the fidelity and robustness of cerebral organoids as a model for cortical development.

overall_design: We performed scATAC-seq and scRNA-seq on cortical organoids derived from 3 human pluripotent stem cell lines (13234, H28126, H1) at three different timepoints of differentiation using the 10x Genomics Chromium Gene Expression and ATAC solutions. We performed a separate experiment with 13234-derived cerebral organoids in which 3 different treatment condiitons were used (Vitamin A treatment, no Vitamin A, and DEAB). These organoids were processed at 10 weeks for scRNA-seq using the 10x Genomics Chromium Gene Expression solution.

middle: S

first: Tomasz

last: Nowakowski


title: miRNA profiling in mouse peritoneal macrophages from macrophage-specific NFATc3 transgenic mice and their control littermates

status: Public on Dec 04 2020

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

summary: We generated NFATc3 macrophage-specific transgenic mice (NFATc3MTG) using the piggyback Transposon. Peritoneal macrophages were isolated from NFATc3MTG mice and their control littermates (wild-type), and the miRNA expression profile was analyzed with deep sequencing.

overall_design: NFATc3MTG and wild-type mice (10-weeks old) were injected with 1 mL 3% thioglycolate. Peritoneal macrophages were isolated via peritoneal lavage 4 days later and cultured in medium for 24 h. Cells were harvested, RNA isolated, and miRNA sequencing performed using the Illumina HiSeq. miRNA library was built using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Beverly, MA) and run on the HiSeq 2500 (Illumina) in 50 bp single-end reads.


title: AI-guided Discovery of a Paradoxical Immune Response in Fatal COVID-19 (Ileum)

status: Public on Dec 07 2020

city: La Jolla

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

summary: We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. The signature was surprisingly conserved in all viral pandemics, including COVID-19, inspiring the nomenclature ViP-signature. A subset of 20-genes classified disease severity in respiratory pandemics. The ViP signatures pinpointed airway epithelial and myeloid cells as the major contributors of an IL-15 cytokine storm, and epithelial and NK cell destruction as determinants of severity/fatality. They also helped formulate precise therapeutic goals to reduce disease symptoms and severity. Thus, the ViP signatures provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool in our armamentarium to rapidly assess disease severity and vet candidate drugs.

overall_design: Human Ileum organoid were infected with SARS-CoV-2 for 48h and 72h.

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Transcriptional profiling of liver from mice treated with Toll-like receptor 5 agonists

status: Public on Dec 24 2020

city: Buffalo

first: Andrei

last: Gudkov

state: NY

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

summary:
Entolimod, a pharmacological derivative of the natural Toll-like receptor 5 (TLR5) agonist flagellin, has strong therapeutic potential for several indications including radioprotection and cancer immunotherapy. However, in Phase 1 studies, entolimod induced a rapid neutralizing immune response, presumably due to flagellin-reactive immune memory derived from life-long exposure of adult humans to flagellated enterobacteria. Since applications requiring repeated dosing could be precluded by entolimod’s neutralizing antigenicity and immunogenicity, we used structure-guided reengineering to develop a new, substantially deimmunized entolimod variant, GP532.
We used RNAseq-based analysis of global gene expression profiles in C57BL/6 mice following systemic administration of entolimod vs GP532 to evaluate the biocomparability of the two drugs. In this experiment, we used wild type (WT) and TLR5-/- mice (on the same genetic background) to address the TLR5-dependence/specificity of responses and focused on the liver since it was previously defined as the major organ responsive to TLR5 systemic administration in mice . Analysis of livers collected 30 minutes after injection of entolimod or GP532 was aimed at assessing direct primary TLR5 responses, while a 24-hour time point was included (for wild type mice) to define long-term overall (direct and indirect) effects of TLR5 activation.
Overall, our RNAseq-based analysis of the effects of entolimod and GP532 on transcription confirmed our expectations of their mechanism of action and overall biocomparability. These results establish GP532 as a highly optimized TLR5 agonist suitable for multi-dose therapeutic regimens and for patients with high titers of preexisting flagellin-neutralizing antibodies.

overall_design: Gene expression profiles were generated by deep sequencing for livers of WT and TLR5-/- C57BL/6 mice treated with vehicle, entolimod or GP532. Livers were collected at 30min and 24h for WT mice and at 30 min only for TLR5-/-. All experiments were performed in triplicates with the exception of TLR5-/- liver treated with entolimod at 30 minutes after administration which was performed in duplicate.

first: Craig

last: Brackett

first: Ivan

last: Molodtsov


title: Chromatin accessibility associates with protein-RNA correlation in human cancer

status: Public on Dec 03 2020

city: Palo Alto

first: Akshay

last: Sanghi

address: 3165 Porter Drive

institute: Stanford University

summary: This work describes a previously unreported link between the chromatin states and protein abundance in cancer. We curated and studied a novel cohort of human thyroid tumors that allowed us to identify chromatin features that directly regulate protein expression. We believe this is the first study to establish chromatin states that reflect protein abundances in human cancer.

overall_design: Examination of chromatin accessibility and gene expression in thyroid cancer

first: Michael

last: Snyder


title: LFY is pioneer transcription factor [MNase-seq]

city: Philadelphia

first: Doris

last: Wagner

state: PA

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania

summary: This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated   LFY-GR   triggers   synchronous   and   abundant   flower   induction (PMID: 15225291). We combined  LFY ChIP-seq,  MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.

overall_design: MNase   seq   of   35S:LFY-GR   root   explants.   Tissues   were   treated   with dexamethasone (after LFY binding) or mock (before LFY binding) solution. Two   MNase   concentrations   were   used:   low   MNase   treatment,   which preserve fragile nucleosomes and standard (high) MNase treatment, in which fragile nucleosomes are lost. Two biological replicates were sequenced for each condition.

first: Samantha

last: Klasfeld

first: Run

last: Jin


title: LFY is pioneer transcription factor [RNA-seq]

summary: This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated LFY-GR triggers synchronous and abundant flower induction (PMID: 15225291). We combined LFY ChIP-seq, MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.

overall_design: Identification of 35S:LFY-GR induced genes using RNA-seq in the Ler ecotype of Arabidopsis thaliana. Root explants were treated with mock or dexamethasone solution for 1hr, 6hr or 24hr. Two biological replicates were sequenced per condition.


title: Genome-wide maps of chromatin state changes in miR-204-3p-overexpressed human monocyte-derived macrophages (HMDMs)

summary: We compared histone modification states between miRNA-204-3p and mimics negative control transfected HMDMs through ChIP. sequencing

overall_design: Examination of 2 different histone modifications in HMDMs.


title: PB-Cre/Pten/Smad4 mouse prostate cancer micorarray for CRPC and lung metastasis studies

status: Public on Dec 18 2020

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

department: Biological Sciences

institute: University of Notre Dame

summary:
PB-Cre/Pten/Smad4 is a transgenic mouse model of metastatic prostate adenocarcinoma (PMID: 21289624).  To study the transcriptomic alterations associated with castration-resistant prostate cancer (CRPC), the PB-Cre/Pten/Smad4 males with established prostate cancer were treated with surgical castration followed by enzalutamide-admixed diet. After about 4 weeks, dorsolateral prostate (DLP) lobes of treatment-naïve prostate tumors (N=2) and CRPC tumors (N=3) were harvested and extracted for RNA purification and microarray profiling.
To further study the transcriptomic changes associated with lung metastases of the PB-Cre/Pten/Smad4/mTmG CRPC model, the PB-Cre/Pten/Smad4 males with established prostate cancer were treated with surgical castration followed by enzalutamide-admixed diet. About 3 months later, from one mouse anterior prostate (AP), dorsolateral prostate (DLP), ventral prostate (VP) and GFP+ lung metastasis nodules were each harvested for RNA purification and microarray profiling.

overall_design: The samples were all harvested from PB-Cre/Pten/Smad4 male mice. For the study of CRPC, treatment-naïve prostate tumors (N=2) and CRPC tumors (N=3) were profiled. For the study of CRPC primary tumor and lung metastasis, 1 AP sample, 1 DLP sample, 1 VP sample and 1 lung metastasis sample were profiled, all from one mouse.


title: Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltansferase with CRISPR/dCas9

status: Public on Nov 26 2020

city: Montreal

first: Moshe

last: Szyf

state: QC Quebec

address: 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology & Therapeutics

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: Although associations between DNA methylation and gene expression were established four decades ago, the causal role of DNA methylation in gene expression remains unresolved. Different strategies to address this question were developed; however, all are prone to confounds and may fail to disentangle cause and effect. We developed here a highly effective new method using only deltaCas9(dCas9):gRNA site-specific targeting to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzymatic activity, enabling examination of the role of DNA demethylation per se in living cells. We show that the extensive induction of gene expression achieved by TET/dCas9-based targeting vectors is confounded by DNA methylation-independent activities, inflating the role of DNA methylation in the promoter region. Using this new method, we show that in several inducible promoters, the main effect of DNA methylation is silencing basal promoter activity. We find no credible evidence of off-target DNA demethylation as a consequence of gRNA binding. Thus, the effect of demethylation of the promoter region in these genes is small, while induction of gene expression by different inducers is large and DNA methylation independent. In contrast, targeting demethylation to the pathologically silenced FMR1 gene targets robust induction of gene expression. We also found that standard CRISPR/Cas9 knockout generates a broad unmethylated region around the deletion, which might confound interpretation of CRISPR/Cas9 gene depletion studies. In summary, this new method could be used to reveal the true extent, nature, and diverse contribution to gene regulation of DNA methylation at different regions.

overall_design: Whole genome bisulfite sequencing (WGBS) of 5 treatment conditions of NIH-3T3 cells in triplicates, including control untreated NIH-3T3 cells and those expressing (by lentivirus mediated gene-transfer) dCas9 (thereafter removed by lentiviral Cre recombinase) in combination with either a scrambled non-targeting guideRNA (gRNAscr) or a guideRNA targeting the transcription start site of the shorter isoform of IL33 (gRNA3) as well as those expressing dCas9 fused to human TET1 (dCas9-TET) with the same two guideRNAs.

first: Daniel

last: Sapozhnikov


title: p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)

status: Public on Dec 09 2020

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

summary: To analyze the epigenomic landscape of neurodegeneration caused by ALS-associated protein aggregation, we developed a modified version of ATAC-seq that works on primary neurons. We discovered that C9orf72-ALS/FTD associated poly(PR) activated a remarkably specific signature of chromatin accessibility, involving transcriptional targets of the tumor suppressor gene p53. Our findings reveal an unexpected role of p53 as a mediator of neurodegeneration elicited by poly(PR) and provide an example of how ATAC-seq can now be applied to neurons to define mechanisms of neurodegeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA and DNA were isolated from primary neurons treated for 20, 40 and 60h with either GFP, (PR)50, TDP-43 or untreated. Neurons were grown on 12 well plates each with 450,000 neurons and for each condition 4 biological replicates were pooled together and then split into 2 groups. To obtain RNA from the same neurons that were used for ATAC-seq, we performed sequential lysis. Neurons were first lysed in ATAC-seq resuspension RSB buffer, followed by sequential RNA extraction and isolation in RLT buffer of the QIAGEN RNeasy Plus Micro Kit (QIAGEN), according to the manufacturer’s protocol. In brief, cells were lysed, homogenized, and loaded on a genomic DNA (gDNA) eliminator column. After removal of genomic DNA, RNA was purified using RNeasy spin columns. RNA quantity and purity were determined by optical density measurements of OD260/280  and OD230/260  using a NanoDrop spectrophotometer. Structural integrity of the total RNA was assessed using a 2200 TapeStation Instrument with RNA ScreenTapes (Agilent Technologies, Santa Clara, CA). mRNA libraries were prepared using a SureSelect Strand-Specific RNA Library Preparation kit for Illumina (G9691B) on an Agilent Bravo Automated Liquid Handling Platform, following the manufacturer’s protocol. Libraries were sequenced on an Illumina HiSeq 4000. For the ATACseq Primary cortical neurons treated for 20, 40 and 60h with either GFP, (PR)50, TDP-43 or untreated, were pretreated with 200 U/ml DNase (Worthington) for 30 min at 37°C to remove free-floating DNA and to digest DNA from dead cells. This medium was then washed out, and the cells were washed in cold PBS four times. To avoid neuronal cell death that is associated with trypsinization, neurons were directly lysed in 1ml of cold ATAC-seq resuspension buffer (RSB; 10mM Tris-HCl pH 7.4, 10mM NaCl, and 3mM MgCl2 in water, containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin) on ice for 10 min. After lysis cells nuclei were collected and counted, 50,000 viable cells were centrifuged at 500xg for 5 min in a pre-chilled (4°C) fixed-angle centrifuge. After centrifugation, supernatant was carefully aspirated, with two pipetting steps; The remaining 100μl of supernatant was carefully aspirated by pipetting with a P200 pipette tip to avoid the cell pellet. Cell pellets were then resuspended in 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin), and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 RCF in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was carefully removed with two pipetting steps, as described before, and nuclei were resuspended in 50μl of transposition mix (25μl 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5μl transposase (100 nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20, and 5μl water) by pipetting up and down six times. Transposition reactions were incubated at 37°C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator columns. The complete eluate underwent PCR, as follows. After initial extension, 5 cycles of pre-amplification using indexed primers (Buenrostro et al., 2015) and NEB Next High-Fidelity 2X PCR Master Mix (NEB) were conducted, before the number of additional cycles was assessed by quantitative PCR using SYBR Green. Typically, 7-9 additional cycles were run. The final library was purified using a MinElute PCR kit (QIAGEN) and quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a High Sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent). All libraries were sequenced using 150bp Nextseq High Output Cartridge kits and a Nextseq 500 sequencer (Illumina).

first: Maya

last: Maor-Nof

first: Zohar

last: Shipony

first: Jacob

last: Blum

first: William

last: Greenleaf

first: Aaron

middle: D

last: Gitler


title: Unveiling the heterogeneity of NKT cells in the liver through single cell RNA sequencing

status: Public on Nov 18 2020

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
CD1d-dependent type I NKT cells, which are activated by lipid antigen, are known to play
important roles in innate and adaptive immunity, as are a portion of type II NKT cells. However,
the heterogeneity of NKT cells, especially NKT-like cells, remains largely unknown. Here, we report the profiling of NKT (NK1.1+CD3e+) cells in livers from wild type (WT), Jα18-deficient and CD1d- deficient mice by single-cell RNA sequencing. Unbiased transcriptional clustering revealed distinct
cell subsets. The transcriptomic profiles identified the well-known CD1d-dependent NKT cells and defined two CD1d-independent NKT cell subsets. In addition, validation of marker genes revealed
the differential organ distribution and landscape of NKT cell subsets during liver tumor progression. More importantly, we found that CD1d-independent Sca-1−CD62L+ NKT cells showed a strong ability to secrete IFN-γ after costimulation with IL-2, IL-12 and IL-18 in vitro. Collectively, our findings provide a comprehensive characterization of NKT cell heterogeneity and unveil a previously undefined functional NKT cell subset.

overall_design: NKT cells  were isolated from WT, Jα18-deficient and CD1d-deficient  mice, and were profiled by scRNA-seq.

first: Hao

last: Shen

first: Chan

last: Gu

first: Xiaolong

last: Liu


title: Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer [ChIP-seq]

status: Public on Nov 17 2020

city: Shanghai

first: Huanlong

last: Qin

state: Shanghai

address: 301 Yan Chang Road

department: Gastrointestinal Surgery

institute: Shanghai Tenth People’s Hospital Affiliated to Tongji University

summary: We interrogated global super-enhancer landscape and sought to discover master regulators governing the liver metastasis of colorectal cancer (CRC). Using de novo analysis, we predicted motif enrichment of master transcription factor in super-enhancers. We show that transcription factor-binding sites of hepatocyte nuclear factor 1 (HNF1) family are enriched at super-enhancers identified in cell lines derived from liver metastases, but not those derived from primary tumors. Using ChIP-Seq of acetylated H3K27, the enrichment of HNF1 binding motifs in super enhancers was found in a cell line derived from xenografted liver metastasis but not the parental cell line. The prediction method was further extended to pancreatic cancer where liver metastasis is also a common finding, and a similar enrichment of HNF1 family motif in super-enhancers was found. We subsequently showed that HNF1A was prominently expressed and significantly upregulated in metastatic cell lines and clinical specimens of liver metastases. Collectively, our study implicates HNF1A as a master transcription factor involved in shaping global super-enhancer landscape in CRC liver metastasis.

overall_design: Examination of H3K27ac profile in KM12SM and parental KM12C cells

first: Chunmiao

last: Cai

first: Dexi

last: Bi

first: Hu


title: Sestrins regulate age-induced deterioration of muscle stem cell homeostasis [RNA-seq]

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

summary: We utilize RNA-Seq to evaluate how loss of Sestrin1,2, a conserved set of stress-inducible proteins, alters the metabolism and quiescent state of young (2-3 months) Muscle Stem Cells (MuSCs) during the regenerative response.

overall_design: Bulk RNA-Seq at 0, 7, and 21 days post-injury for both wild-type (WT) and Sestrin1,2 knockout (SKO) MuSCs. 2 replicates are provided per condition at each timepoint.

first: Benjamin

last: Yang

first: Jesus

last: Castor-Macias

first: Paula

last: Fraczek

first: Lemuel

last: Brown

first: Myungjin

last: Kim

first: Susan

last: Brooks

first: Jun

middle: H

last: Lee


title: RNA-seq of mouse lung tissue from amiodarone and/or dabigatran treated animals

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyoto University

summary: Interstitial lung disease (ILD) is a group of respiratory disorders characterized by chronic inflammation and fibrosis of the pulmonary interstitial tissues. Although the etiology of ILD remains unclear, some drug treatments are one of the primary causes of ILD. In the present study, we analyzed FDA Adverse Event Reporting System and JMDC insurance claims to find a coexisting drug that reduced the incidence of ILD associated with use of an anti-arrhythmic agent, amiodarone, and found that the thrombin inhibitor dabigatran prevented the amiodarone-induced ILD in both clinical datasets. In an experimental validation of the hypothesis, a long-term, oral treatment of mice with amiodarone caused a gradual decrease in the body weight caused by respiratory insufficiency. In the lung of amiodarone-treated mice, infiltration of macrophages and interstitial thickening were observed in parallel with a delayed upregulation of platelet-derived growth factor receptor α gene. In contrast, co-treatment with dabigatran significantly attenuated these amiodarone-induced changes representing ILD. These results suggest that dabigatran is effective in preventing the drug-induced ILD. This combinatorial approach of drug repositioning based on clinical big data will pave the way for finding a new treatment with high clinical predictability and a well-defined molecular mechanism.

overall_design: Lung mRNA profiles of vehicle-, amiodarone-, dabigatran-, or amiodarone+dabigatran-treated mice.

first: Soni

last: Siswanto

first: Shuji

last: Kaneko


title: Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing

status: Public on Dec 14 2020

city: Bethesda

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: Recently, multiple single cell assays were developed for detecting histone marks at the single cell levels. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11K and 45K non-redundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single cell data are specifically correlated with the cell types annotated from H3K27me3 single cell data.  Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.

overall_design:
Profiling genome-wide H3K4me3 with multiplex indexing tecnique at the single cell level

Please note that processed data have been updated on Feb 26, 2021.

first: Wai

last: Ku

first: Lixia

last: Pan


title: Genome-wide mapping of RNAPII and its phosphoisoforms in Plasmodium falciparum

status: Public on Dec 30 2020

first: Mark

middle: Stephen

last: Featherstone

address: 60, Nanyang Drive

department: School of Biological Sciences

summary: RNAPII ChIP seq was carried out with various phospho antibodies and compared and correlated with the RNA -seq expression data from the same stage sample

overall_design: RNAPII ChIP -seq was carried out with anti-CTD, anti-Ser5-P, anti-Ser2/5-P and N20 antibodies at three different stages, ring, trophozoites and schizonts across the inter-erythrocytic developmental cycle (IDC) of Plasmodium falciparum. RNAPII binding was correlated with mRNA expression levels generated by RNA Seq. RNA- seq experiment includes three biological replicates.

first: Ragini

last: Khandelia

first: Aarthi

last: Mohan

first: Zhu

last: Lei

first: Uthra

last: Balasubramaniam

first: Jie

last: Zheng

first: Zbynek

last: Bozdech


title: The effect of mitochondrial uncoupling on triple-negative breast cancer

status: Public on Dec 10 2020

city: Baton Rouge

first: John

middle: P

last: Kirwan

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: Examination of two different mitochondrial uncouplers of human triple-negative breast cancer cells

overall_design: MDA-MB-231 cells were treated with either 0.1% DMSO Vehicle or 20uM BAM15 for 16 hours and RNA was isolated for cellular transcriptome analysis.

first: Elizabeth

last: Zunica

first: L

last: Gilmore

first: Jasleen

last: Kaur

first: Sara

last: Webb

first: Richard

last: Carmouche

first: Christopher

last: Axelrod

first: William

middle: T

last: King


title: Replacing the SpCas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope

status: Public on Nov 12 2020

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

summary: Base editors are RNA-guided deaminases that enable site-specific nucleotide transitions. The targeting scope of these Cas-deaminase fusion proteins critically depends on the availability of a protospacer adjacent motif (PAM) at the selected genomic locus, and is limited to a window within the CRISPR-Cas R-loop where single stranded (ss)DNA is accessible to the deaminase. Here, we reason that the Cas9-HNH nuclease domain sterically constrains ssDNA accessibility, and demonstrate that omission of this domain expands the editing window. By exchanging the HNH nuclease domain with an adenosine deaminase, we furthermore engineer adenine base editor variants (HNHx-ABE) with PAM-proximally shifted editing windows. HNHx-ABEs are substantially reduced in size, and expand the targeting scope of base editors. Our finding that the HNH domain is replaceable could moreover benefit future protein engineering efforts, where Cas9 operates together with other enzyme domains.

overall_design: Refer to individual Series

first: Lukas

last: Villiger

last: Schmidheini

first: Gerald

last: Schwank


title: RHEUMATOID ARTHRITIS SYNOVIAL MICROENVIRONMENT INDUCES METABOLIC AND FUNCTIONAL ADAPTATIONS IN DENDRITIC CELLS

status: Public on Nov 05 2020

city: la jolla

first: vipul

last: bhargava

address: 9500 gilman drive

institute: ucsd

summary: Rheumatoid Arthritis (RA) is a chronic autoimmune disease which causes degradation of cartilage and bone. It is well appreciated that the pathogenic hallmark of RA is the mass influx of inflammatory cells into the joint. However, the role dendritic cells (DC) may play in this inflammatory milieu is still relatively unexplored. Moreover, the contribution this unique synovial microenvironment has on DC function and maturation is still unknown. Using monocyte-derived DC (MoDC), we established an in vitro model to recapitulate the synovial microenvironment to explore DC maturation. MoDC treated with conditioned media from ex vivo synovial tissue biopsy cultures (ECM) have increased expression of proinflammatory cytokines, chemokines and adhesion molecules. ECM treated DC have increased expression of CD83 and CCR7 and decreased expression of CCR5 and phagocytic capacity, suggestive of heightened DC maturation. ECM induced maturation is concomitant with altered cellular bioenergetics, whereby increased expression of glycolytic genes and increased glucose uptake are observed in ECM treated DC. Collectively, this results in a metabolic shift in DC metabolism in favor of glycolysis. These adaptations are in-part mediated via STAT3 as demonstrated by decreased expression of proinflammatory cytokines and glycolytic genes in ECM treated DC in response to STAT3 inhibition. Finally, to translate this data to a more in vivo clinically relevant setting, we interrogated a previously published synovial DC dataset and identified enhanced expression of glycolytic genes in synovial DC compared to DC in circulation. Collectively, our data suggests that the synovial microenvironment in RA contributes to DC maturation and metabolic reprogramming.

overall_design: 9 samples

first: Vipul

last: Bhargava

first: Mary

last: Canavan


title: Chromosomal loop engineering in human beta globin locus (CUT & RUN)

status: Public on Oct 30 2020

city: Houston

first: Xiaotian

last: Zhang

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

summary: We have engineered the 3 prime HS1 CTCF binding site at the human beta globin gene locus in HUDEP-2 cells and performed RNA-seq/ChIP-seq/ATAC-seq as well as HiC and capture HiC to dissect its potential in regulating gene expression

overall_design: We have deleted 3 prime HS1 CTCF binding site in HUDEP-2 cells with CRISPR/Cas9 and inverted 3 prime HS1 CTCF binding site with CRISPR/Cas9-mediated HDR. In each condition, we have obtained two independent clones for the 3’HS1 CTCF binding site deletion and the 3 prime HS1 CTCF binding site inversion.

first: Pamela

last: Himadewi

first: Haley

last: Gore


title: Chromosomal loop engineering in human beta globin locus (Hi-C)


title: Chromosomal loop engineering in human beta globin locus (RNA-Seq)


title: Chromosomal loop engineering in human beta globin locus (ChIP-Seq)


title: Replacing the SpCas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope [RNA-seq]

overall_design: total RNA-seq data from 3 replicates each

middle: L


title: Chromosomal loop engineering in human beta globin locus (ATAC-Seq)


title: RNA expression in NSUN6 knockout cells

status: Public on Oct 29 2020

city: Guangzhou

first: Rui

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary: mRNA m5C, which has recently been implicated in the regulation of mRNA mobility, metabolism, and translation, plays important regulatory roles in various biological events. Two types of m5C sites are found in mRNAs. Type I m5C sites, which contain a 3’G-rich triplet motif and locate in the 5’ end of hairpin structures, are methylated by NSUN2. Type II m5C sites contain a 3’UCCA motif and locate in the loops of hairpin structures. However, their biogenesis remains unknown. Here we identified a novel mRNA methyltransferase that targets Type II m5C sites and generated BS-seq and RNA-seq data to verify our findings.

overall_design: Poly(A)+ RNA of wildtype cells and NSUN6 knocout cells were extracted for RNA-seq measurement.

first: Jianheng

last: Liu

first: Tao

last: Huang

first: Yusen

first: Tianxuan

last: Zhao

first: Xueni

first: Wanying

last: Chen


title: Identifying the impact of NSUN6 mutants on tRNA methylation

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: tRNA BS-seq was performed for  HEK293T cell line, NSUN6 knockout HEK293T cell line, NSUN6 knockout HEK293T cell line rescued by different NSUN6 variants, wildtype flies and NSUN6 knockout flies.


title: Replacing the SpCas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope [DNA-seq]

overall_design: HTS data from >= 3 replicates


title: Chromosomal loop engineering in human beta globin locus

summary: This SuperSeries is composed of the SubSeries listed below.


title: RNA bisulfite sequencing for polysome fractions

overall_design: mRNA BS-seq was performed for different polysome fractions of HEK293T cells


title: CRM1 inhibitor anti-tumor activity is enhanced with salicylates by S-phase arrest and impaired DNA-damage repair

status: Public on Oct 28 2020

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Chromosome region maintenance protein1 (CRM1) mediates protein export from the nucleus and is a new target for anti-cancer therapeutics. Broader application of KPT-330 (Selinexor), a CRM1 inhibitor approved for myeloma, has been limited by toxicity. We found that combining choline salicylate (CS) with low-doses of KPT-330 (K+CS) had potent synergistic activity across blood and solid organ cancers ex-vivo and in-vivo. Mechanistically, K+CS enhances CRM1 degradation, induces potent inhibition of CRM1 mediated nuclear export, and arrests cells in S-phase with simultaneous reduction of Rad51 causing impaired DNA damage repair. K+CS represents a potential new class of therapy for multiple cancer types.

overall_design: JEKO-1 cells were treated with the drug conditions KPT-330, choline salicylate(CS), KPT-330+CS (K+CS) or DMSO control for 48 hours. RNA was extracted using the AllPrep DNA/RNA FFPE kit (Qiagen, Germany). Sequencing libraries were prepared using TruSeq RNA Library Prep kit V2 (Illumina, San Diego, CA) and analyzed on a HiSeq 4000 sequencer (Illumina, San Diego, CA). Sequenced reads were aligned to the hg38 reference using the previously published MAP-RSeq pipeline slightly modified to use the STAR aligner. Gene-level read counts based on Ensembl version 78 were analyzed using edgeR to find differentially expressed proteins. For this, gene counts were normalized using TMM method to remove batch effects. Normalized read counts were compared across experimental groups using a negative binomial generalized log-linear model. A total of four group comparisons were performed: KPT-330 vs. control, CS vs. control, K+CS vs. control and CS vs. KPT-300. For each comparison, genes with an adjusted p-value (Benjamini-Hochberg) ≤ 0.05 and an absolute log2 (fold change)>2.0 were considered as significantly differentially expressed and saved for further analysis.

first: Thomas

last: Witzig

first: Jithma

last: Abeykoon


title: CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10

city: Dallas

first: Siyuan

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

summary: We used CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of a set of immune markers of naïve brain myeloid cells from wild type C57BL/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57BL/6 mice bearing E0771 brain metastases. In each sequencing round, we sequenced a total of four different mouse brains (2 naive and 2 metastasis-burdened). We created an antibody pool consisting of 6 different antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all six samples and finally separate each sample in silico by it's unique hashing antibody.

overall_design:
Naïve brains were obtained from 2-3 month old female C57Bl/6 mice without brain metastases. Brains bearing metastases initiated by carotid injection of E0771 cells were obtained from 2-3 month old female mice (C57Bl/6) with established brain metastases (~2 weeks post injection). Cell suspensions were prepared by percoll gradient centrifugation enrichment to obtain suspensions enriched for immune cells. We created an antibody pool consisting of 6 different ADT antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Genomics Chromium and later prepare one library consisting of all four samples and finally separate each sample in silico by it's unique hashing antibody.
Please note that the ADT-HTO-tags.csv is the bar code table used for CITE-seq-Count software (CITE-seq-Count v1.3.4; https://github.com/Hoohm/CITE-seq-Count).

first: Ian

last: Guldner


title: A Single-Cell Tumor Immune Atlas for Precision Oncology

status: Public on Oct 27 2020

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

summary: The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell resolved tumor immune cell atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we developed SPOTlight, a computational tool that identified striking spatial immune cell patterns in tumor sections. We expect the atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification strategies for prognosis and immuno-therapy response.

overall_design: Single-cell RNA sequencing was performed on two human uveal melanoma cancers, one human ovarian cancer, one human uveal melanoma liver metastasis, one human non-small cell lung cancer brain metastasis (including TCR), two human head and neck cancers and two mice colorectal cancers (one full and one only T cells and TCR)

first: Holger

last: Heyn


title: Bisulfite sequencing for poly(A)+ RNA

overall_design: Poly(A)+ RNA BS-seq was performed for: (1) wildtype cells, including HeLa, HepG2, HEK293T; (2) cells with NSUN2/NSUN6 mutations (HEK29T and HeLa); (3) cells with dysfunction NSUN6 and transfected with NSUN6 variants; (4) seperated cell fractions for HEK293T; (5) fly tissues.


title: LFY is pioneer transcription factor [ChIP-seq]

city: Philadelphia

first: Doris

last: Wagner

address: 103G Carolyn Lynch Laboratory

summary: This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated   LFY-GR   triggers   synchronous   and   abundant   flower   induction (PMID: 15225291). We combined  LFY ChIP-seq,  MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.

overall_design: Identification of genomic regions bound by LFY in root explants identified using 35SLFY-GR in L.er ecotype of Arabidopsis thaliana. ChIP seq was performed using anti LFY antibodies 24 hours after dexamethasone  or mock treatment. Three biological replicates were sequenced for each condition, as were three inputs.

first: Run

last: Jin

first: Samantha

last: Klasfeld


title: NG2 glia-derived GABA release tunes inhibitory synapses and contributes to anxiety-like behavior in chronic social defeat stress

status: Public on Nov 24 2020

first: Xiaoqi

last: Hong

address: 280 South Chongqing Road, Huangpu District, Shanghai, China, 200025

department: Discipline of Neuroscience and Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

summary: NG2 glia, also known as oligodendrocyte precursor cells (OPCs), play an important role in proliferation and give rise to myelinating oligodendrocytes during early brain development. In contrast to other glial cell types, the most intriguing aspect of NG2 glia is their ability to directly sense synaptic inputs from neurons. However, whether this synaptic interaction is bidirectional or unidirectional, or its physiological relevance has not yet been clarified. Here, we report that NG2 glia form synaptic complexes with hippocampal interneurons and that selective photostimulation of NG2 glia (expressing channelrhodopsin-2) functionally drives GABA release and enhances inhibitory synaptic transmission onto proximal interneurons in a microcircuit. The mechanism involves GAD67 biosynthesis and VAMP-2 containing vesicular exocytosis. Further, behavioral assays demonstrate that NG2 glia photoactivation triggers an anxiety-like behavior in vivo and induces anxiety-like behavior in a mouse model of chronic social defeat stress.

overall_design: Single-cell RNA seq of sorted NG2 glial cells of 3-week-old Pdgfrα-creERTM; Rosa26-mGFP mouse

first: Xiao

first: Yabing

last: Yang

first: Xiaoping

last: Tong


title: Sequence- and structure-selective mRNA m5C methylation

first: Rui

last: Zhang


title: Gene expression of UC organoids and UC model organoids (long-term inflammation model) derived from human colonic organoids

status: Public on Oct 26 2020

city: yushima bunnkyoku Tokyo

first: Sho

last: Watanabe

department: gastroenterology

institute: Tokyo medical and dental university

summary:
Gene expression changes  of human colon orgnaoids by 60weeks of inflammatory stimulation in vitro (long-term inflammed organoids) and after 10weeks from the removal of stimulation (inflammation-removed organoids).  GSEA analysis was performed about RNA1-9 (Organoids #1). For the reproducibility of the analysis, GSEA was performed in triplicate. The key molecule for long-term inflammation was extracted from RNA10-12 (Organoids #2).
The comparison of gene expression of organoids derived from normal(RNA1-3) and UC mucosa(RNA13-15). For the reproducibility, the analysis was performed in triplicate.

overall_design: Long-term inflamed organoids vs normal organoids / Inflammation removed organoids vs normal organoids / UC orgnaoids vs normal organoids

first: Kiichiro

last: Tsuchiya


title: A novel patient stratification strategy to enhance the therapeutic efficacy of dasatinib in glioblastoma [Illumina]

status: Public on Oct 20 2020

city: Heidelberg

first: Obada

middle: Taleb

last: Alhalabi

address: Im Neuenheimer Feld 580 - TP3

department: Brain Tumor Translational Targets

institute: German Cancer Research Center DKFZ

summary: Abstract. Background: Glioblastoma is the most common primary malignancy of the central nervous system with dismal prognosis. Differential gene expression classifies IDH-wildtype glioblastoma into three subtypes: proneural, mesenchymal and classical. Dasatinib, an inhibitor of the proto-oncogene tyrosine-protein kinase SRC, is one of many therapeutics that, despite promising preclinical results, has failed to improve overall survival in glioblastoma patients in clinical trials. We examined whether glioblastoma subtypes differ in their response to dasatinib therapy and could hence be used for patient enrichment strategies in clinical trials. Methods: We carried out in silico analyses of the TCGA glioblastoma gene expression data and single-cell RNA-Seq data, in combination with in vitro experiments using glioblastoma stem-like cells (GSCs) derived from primary patient tumors with complimentary gene expression profiling and immunohistochemistry analyses of tumor samples. Results: Patients suffering from the mesenchymal subtype of glioblastoma showed higher SRC pathway activation based on gene expression profiling, and accordingly, mesenchymal cells were more sensitive to SRC inhibition by dasatinib compared to proneural and classical cells. Furthermore, SERPINH1, a heat-shock protein relevant in many cancer entities, was shown to highly correlate with dasatinib response and with the mesenchymal subtype. Notably, SRC phosphorylation status was not able to reliably predict response to dasatinib treatment. Conclusion: This work highlights the need for rational methods of patient selection for clinical trials, and retrospectively sheds light on a possible gene expression subtype-led patient stratification strategy that could have improved the outcome of SRC inhibition in patients and could have implications for future trials.

overall_design: No controls needed, simple gene expression profiling of in vitro cell line models

first: Violaine

last: Goidts


title: A novel patient stratification strategy to enhance the therapeutic efficacy of dasatinib in glioblastoma [Agilent]

overall_design: NCH711d and NCH705 cells were inhibited in three independent experiments with DMSO and 1µM of Dasatinib. After 4 days, RNA was extracted and checked using the same method outlined earlier.

last: . Alhalabi


title: A novel patient stratification strategy to enhance the therapeutic efficacy of dasatinib in glioblastoma

overall_design: Refer to individual Series


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190307_5A]

status: Public on Oct 11 2020

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACA,PL,ILA).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

middle: A

last: Mukamel

first: M

last: Behrens


title: Alcohol dependence in rats is associated with global changes in gene expression in the central amygdala

status: Public on Oct 07 2020

city: Lubbock

first: Brent

middle: Romeo

last: Kisby

address: 3601 4th Street

department: Pharmacology and Neuroscience

institute: TTUHSC

summary:
Here, we examined the effects of alcohol on global gene expression in the CeA using a chronic intermittent ethanol (CIE) vapor model in rats and RNA sequencing (RNA-Seq).
The CIE procedure resulted in robust changes in CeA gene expression during intoxication; as the number of differentially expressed genes (DEGs) was significantly greater than those expected by chance.
Over-representation analysis of cell types; functional groups and molecular pathways revealed biological categories potentially important for the development of alcohol dependence in our model.

overall_design: Studying the effects of Chronic alcohol exposure effects on global gene expression in the Central Nucleus of the Amygdala.

first: Igor

last: Ponomarev


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190219_9J]

status: Public on Oct 08 2020

first: Joseph

middle: R

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (DG).

last: Zhang

middle: M


title: Comparative transcriptomic analysis of races 1, 2 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

status: Public on Oct 22 2020

city: MELBOURNE

first: Saidi

middle: Rahina

last: Achari

state: VICTORIA

address: 5 RING ROAD, BUNDOORA

department: Applied Systems Biology

country: Australia

institute: La Trobe University

summary:
Background: The fungal pathogen, Fusarium oxysporum f.sp. pisi (Fop) causes fusarium wilt in peas. Races 1, 2, 5 and 6 are responsible for the majority of the economic losses globally. These are the only races present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales however, there has been no Fop-pea pathosystem studies.
Results: A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcript analysis revealed differences in the differentially expressed genes (DEGs) in the Fop races, potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes,  CAZymes and effector-like proteins were expressed in race 2. Race 6 had expressed the least number of genes during infection.
Conclusion: Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.

overall_design: 48 samples

first: Jatinder

last: Kaur

first: Ross

middle: C

last: Mann

first: Tim

last: Sawbridge

first: Brett

last: Summerell

first: Jacqueline

last: Edwards


title: Genome-wide transcriptome profiling of primary human uterine leiomyoma cell populations

status: Public on Oct 01 2020

city: Chicago

first: Shimeng

last: Liu

state: Illinois

address: 320 East Superior Street

institute: Northwestern University

summary: Uterine leiomyomas (LM) affect up to 80% of all reproductive-age women. LM growth requires progesterone, progesterone receptor (PGR), and the maintenance and proliferation of a small (5%) stem cell population. Stem cell activation and differentiation are driven by DNA methylation and nuclear hormone receptor action, but crosstalk between these mechanisms remains unclear. We performed an integrated analysis of the transcriptome and epigenetic landscape of LM cells at three differentiation stages and the PGR cistrome of whole LM tissue. The PGR-deficient stem cell population harbored a unique methylation landscape, with hypermethylation at the PGR gene locus and PGR-binding regions, which suppressed stem cell responsiveness to progesterone. The DNA methylation inhibitor 5’-Aza upregulated the expression of PGR and its target genes by stimulating PGR recruitment to the targeted gene loci, and significantly depleted the LM stem cell population and its tumor-initiating capacity.  We herein provided mechanistic insights via therapeutically accelerating the stem cell differentiation process of a hormone-sensitive tumor.

overall_design: Genome-wide transcriptome mapping of human primary LM cell populations using RNA-Seq

first: Ping

last: Yin

first: Serdar

last: Bulun


title: Genome-wide H3K4me3 and H3K27Ac profilings of primary human uterine leiomayoma (LM) cell populations

overall_design: Genome-wide H3K4me3 and H3K27Ac profilings of human primary uterine leiomayoma cell populations using native histone ChIP-Seq


title: Exploring the molecular mechanism of action of a mono-herbal formulation of Ayurveda Cesamplous pareira

status: Public on Sep 30 2020

city: Delhi

first: Mitali

last: Mukerji

address: Mathura Road

institute: CSIR-IGIB

summary: Drugs used in traditional medicine are multisystemicand hence are amenable to repurposing. This coupled with the history of safe usage make it possible for practitioners to rapidly evolve therapies for contemporary diseases. We provide a unique framework  that  combines principles of Ayurveda  with transcriptome signatures of drugs, disease and connectivity map that provides a molecular basis for the traditional uses as well as novel leads for drug repurposing. This study has assumed immense importance as we demonstrate its application in a herbal extract of Cissampelos pareira (Cipa) traditionally used to treat diverse disorders such as female reproductive disorders and fevers, for repurposing in a contemporary pandemic, COVID-19. Gene expression studies using gene ontology and GSEA on MCF7 cell lines treated with Cipa extract reveal downregulation of pathways linked to lipid metabolism, protein processing and estrogen response. Estradiol and tamoxifen binding domain of estrogen receptor alpha is shared by nearly 38 constituents of Cipa having ERα BE ranging from -10.2 to -6.1KJ/mole. Transcriptome signatures were analysed and queried in connectivity map (clue.io) show positive connectivity with protein synthesis inhibitors such as Emetine (99.61), Cycloheximide (99.86) and Homoharringtonine (99.51). Cipa shows a very high positive connectivity (>90) with knockdown signature of RPL7 (99.92), UBA52 (99.76) and RPS6 (98.63) that are linked to protein synthesis and anti-viral mechanisms. When the cmap interface was used to query the links between Cipa and COVID19 signatures we found that CIPA signatures are opposite to COVID-19 BALF signatures in connectivity map, which is also resonated in literature as CIPA transcription signatures intersect with implicated molecular pathways and prioritized family of compounds envisaged for COVID-19 from diverse resources.

overall_design: MCF cells treated with three doses of aqeuous extract of Cissampelos pareira and one vehicle control

first: Madiha

last: Haider

first: Dhwani

last: Dholakia

first: Bhavana

last: Prasher


title: Single cell transcriptomic profile of thymic CD21-CD35- B cells in human neonates

city: New York

first: Hector

last: Cordero

address: 650W 168th Street

institute: Columbia University

summary: We have demonstrated that thymic B cells, and more concretely CD21-CD35-, are highly heterogeneous in human neonates. To unravel the heterogeneity, we sorted and analyzed the transcriptome by single-cell RNA sequencing the CD21-CD35- B cell subset in six human donors of 4 days and 4 months old.

overall_design: Examination of single cell transcriptome of thymic CD21-CD35- B cells in human neonates by single cell RNA-sequencing.

first: Emmanuel

last: Zorn


title: Transcriptomic profile of cord blood B cells and thymic B cell subsets in human neonates

summary: We reported two major thymic B cell subsets (CD21+CD35+ and CD21-CD35-) with different morphology, functions and transcriptome profile. For this purpose, mRNA was extracted from cord blood CD19+ B cells and thymic B cells (CD21+CD35+ and CD21-CD35-) from neonatal donors ranged between 1 day and 4 months and sequenced using Illumina HiSeq4000.

overall_design: Examination of transcriptomic profile of cord blood B cells and two subsets of thymic B cells (CD21+CD35+ and CD21-CD35-) in human neonates by RNA-sequencing.


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190212_9H]

status: Public on Oct 02 2020

last: Ecker

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (CA).

first: Hanqing

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

last: He

first: Huaming

last: Chen

first: Zhuzhu

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190205_6D]

first: Joseph

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (PIR).

last: Liu

last: Zhang


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190205_5A]


title: Genome-wide DNA methylation mapping of primary human uterine leiomyoma cell populations

first: Shimeng

overall_design: Genome-wide DNA methylation mapping of human primary uterine leiomayoma cell populations using MethylCap-Seq

first: Ping

last: Yin

first: Serdar

last: Bulun


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190131_6D]

last: Ecker

first: Hanqing

first: Chongyuan

last: Luo


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190214_11E]

first: Angeline

last: Rivkin

first: Anna

last: Bartlett


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190214_11F]

status: Public on Oct 05 2020

first: Jacinta

last: Lucero

last: Nery

first: Andrew